Microarray data were useful in disease diagnosis and prognosis. Most approaches to the computational analysis of gene expression data are functionally significant classification of genes [1, 6, 7]. Fuzzy Neural Network (FNN) is one of the advanced ANN models. FNN system can automatically select the causal gene set consisting of several genes for prediction of the disease diagnosis and prognosis...

Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which mak...

Phylogenetic footprinting is a widely used approach for the prediction of transcription factor binding sites (TFBSs) through identification of conserved motifs in the upstream sequences of orthologous genes in eukaryotic genomes. However, this popular strategy may not be directly applicable to prokaryotic genomes, where typically about half of the genes in a genome form multiple-gene transcript...

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, signifi...

MOTIVATION Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from s...

With the development of genome sequencing for many organisms, more and more raw sequences need to be annotated. Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics. Two classes of methods are generally adopted: similarity based searches and ab initio prediction. Here, we review the development of gene predi...